Publications

📝 Preprints under review

• Dadole, R., Chen, X., Sandoval, J., Venon, A., Criado, M., Delprouve, N., Remoué, C., Chollet, S., Hansart, A., Kirisits, T., Ursu, T.M., Roman, A., Volk, G.M., Alins, G., Marchadier, E., Conde e Silva, N., Avia, K., Bazot, S., Cornille, A. (2026). Climate drives plasticity and genetic adaptation in apple trees. bioRxiv.
• Nie, Y., Chen, X., Saidi, S., Bourgeois, Y., Venon, A., Confais, J., Mesnil, A., Liu, S., Gao, Y., Ni, J., Bai, S., Gao, L., Li, G., Hoefer, M., Francillonne, N., Roman, A., Lukács, L., Denancé, C., Akagi, T., Nersesyan, A., Papikyan, A., Gabrielyan, I.G., Abdollahi, H., Bassil, N.V., Steffensmeier, S., Alix, K., Teng, Y., Cornille, A. (2025). Contrasting genomic routes to domestication in Occidental and Oriental pears. bioRxiv.
• Mesnil, A., Castric, V., Lombardi, G., Monniaux, M., Saidi, S., Chen, X., Marande, W., Confais, J., Fuchs, A.-L., Dapena, E., Venon, A., Tsuchimatsu, T., … & Cornille, A. (2025). Genomic architecture of the self-incompatibility locus in apple provides insights into the evolution of collaborative non-self recognition. bioRxiv.
• Lougmani, C., Mesnil, A., Fahmy, R., Decroocq, V., Bui, Q.T., Liu, S., Chen, X., Chague, A., Venon, A., Chagné, D., Eduardo, I., Alix, K., Cornille, A. (2025). Genomic footprints of domestication in almond (Prunus dulcis). bioRxiv.

📝 Peer-Reviewed Publications

• Criado, M., Brisson, M., Alix, K., Bourgeois, Y., François, O., Marchadier, É., Cornille, A. (2026). Genomic forecasting for climate-resilient fruit trees. New Phytologist, 251 (4), 1640 – 1653.
• Chen, X., Dadole, R., Avia, K., Venon, A., Brisson, M., Remoue, C., Zhang, D., Gabrielyan, I., Nersesyan, A., Roman, A., Ursu, T., Alhmedi, A., Bylemans, D., Belien, T., Rousselet, A., Le Guilloux, M., Dapena, E., Durel, C.-E., Kirisits, T., Volk, G., Didelot, F., Lemarquand, A., Hance, T., & Cornille, A. (2026). Gene flow from the European wild apple and selection shaped the domesticated apple (Malus domestica Borkh.) genome. Current Biology , 36, 1–15.
• Khadari, B., Kakenov, S., Achtak, H., Charafi, J., Chalak, L., Santoni, S., Kjellberg, F., Cornille, A. (2025). Diffuse and regionally structured domestication of the common fig (Ficus carica L.) in the Mediterranean Basin. Horticulture Research, uhag113.
• Blanchard, I., Bui, Q.T., Mergez, A., Denni, S., Cornille, A., Groppi, A., Confais, J., Duvaux, L., Decroocq, V., Linard, B. (2025). Building pangenomes for domesticated and wild tree species: genomic complexity and strategies. Horticulture Research, uhag104.
• Decroocq, S., Cornille, A., Cadillon, J., Dlalah, N., Duval, H., Tricon, D., Quilot, B., Chague, A., Eduardo, I., Batlle, I., Drogoudi, P., Küden, A., Asma, B.M., Kostritsyna, T., Decroocq, V. (2025). Insights into the almond domestication history. Evolutionary Applications, 18(10), 1749–1764.
• Olvera-Vazquez, S., Chen, X., Mesnil, A., Meslin, C., Almeida-Silva, F., Confais, J., Bourgeois, Y., Lombardi, G., Lougmani, C., Alix, K., Francillonne, N., Choisne, N., Cauet, S., Simon, J.C., Buchard, C., Rodde, N., Ogereau, D., Mottet, C., Degrave, A., Segura, E., Carbone, A., Barrès, B., Jacquin-Joly, E., Marande, W., Lavenier, D., Legeai, F., Cornille, A.* (2025). Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids. Molecular Biology and Evolution. *Directed the work.*
• Wang, R., Deng, C.H., Cornille, A. et al. (2025). Characterisation of the Gillenia S-locus provides insight into evolution of the nonself-recognition self-incompatibility system in apple. Scientific Reports, 15, 14630.
• Lucotte, E., Jay, P., Rougemont, Q., Boyer, L., Cornille, A., Snirc, A., Labat, A., Chahine, E., Duhamel, M., Gendelman, J., Ma, W.-J., Hayes, R.K., Perlin, M.H., Hood, M.E., Rodríguez de la Vega, R.C., Giraud, R. (2025). Repeated loss of function at HD mating-type genes and of recombination suppression without mating-type locus linkage in anther-smut fungi. Nature Communications.
• Cai, Y., Gao, X., Mao, J., Liu, Y., Tong, L., Chen, X., Liu, Y., Kou, W., Chang, C., Foster, T., Yao, J., Cornille, A., Tahir, M.M., Liu, Z., Yan, Z., Lin, S., Ma, F., Ma, J., Xing, L., An, N., Zuo, X., Lv, Y., Zhao, Z., Li, W., Li, Q., Zhao, C., Hu, Y., Liu, H., Wang, C., Shi, X., Ma, D., Fei, Z., Jiang, Y., Zhang, D. (2024). Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology. Nature Communications, 15, 10082.
• Kazmareck, T., Chen, X., Fior, S., Venon, A., Roman, A., Ursu, T., Giraud, T., Mezhenskyj, V., Koupilova, K., Hood, M.E., Widmer, A., Cornille, A. (2023). Sequential colonization events with restricted gene flow in a widespread European carnation species. bioRxiv.
• Chen, X., Avia, K., Forler, A., Remoué, C., Venon, A., Rousselet, A., Lucas, G., Kwarteng, A. O., Rover, R., Le Guilloux, M., Belcram, H., Combes, V., Corti, H., Olverà-Vazquez, S., Falque, M., Alins, G., Kirisits, T., Ursu, T. M., Roman, A., … Cornille, A. (2023). Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple (Malus sylvestris (L.) Mill.), a wild relative of the cultivated apple.. Annals of Botany.
• Tenaillon, M. I., Burban, E., Huynh, S., Wojcik, A., Thuillet, A.-C., Manicacci, D., Gérard, P. R., Alix, K., Belcram, H., Cornille, A., Brault, M., Stevens, R., Lagnel, J., Dogimont, C., Vigouroux, Y., & Glémin, S. (2023). Crop domestication as a step toward reproductive isolation.. American Journal of Botany.
• Bina, H., Yousefzadeh, H., Venon, A., Remoué, C., Rousselet, A., Falque, M., […] Cornille, A. (2022). Evidence of an additional center of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool. Molecular Ecology.
• Cornille, A. *+, Tiret, M.*, Salcedo, A.*, Huang, H. R.*, Orsucci, M., Milesi, P., Kryvokhyzha, D., Holm, K., Ge, X.-J., Stinchcombe, J. R., Glémin, S., Wright, S. I., Lascoux, M.+ (2022). The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe. Annals of Botany: Plants.
• Cornille, A.*, Ebert, D., Stukenbrock, E., Rodríguez de la Vega, R., Tiffin, P., Croll, D.*, Tellier, A.* (2022). Unraveling coevolutionary dynamics using ecological genomics. Trends in Genetics.
• Chen, X.*, Cornille, A.*+, Na, A., Xing, L., Ma, J., Zhao, C., Wang, Y., Han, M., Zhang, D.+ (2022). An additional area of apple domestication with crop-wild gene flow, and also cultivation of the local wild apple, in the Caucasus. Molecular Ecology.
• Brisou, G., Piquerez, S. J. M., Minoia, S., Marcel, F., Cornille, A., Carriero, F., Boualem, A., Bendahmane, A. (2021). Induced mutations in SlE8 and SlACO1 control tomato fruit maturation and shelf-life. Journal of Experimental Botany, 72(20), 6920–6932.
• Olvera-Vazquez, S. G., Remoué, C., Venon, A., Grandcolas, O., Azrine, M., Momont, L., […], Jousselin, E., Cornille, A.* (2021). Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa. Peer Community Journal.
• Märkle, J. S., Cornille, A., Fields, P. D., Tellier, A. (2021). Novel genomic approaches to study antagonistic coevolution between hosts and parasites. Molecular Ecology.
• Olvera-Vazquez, S. G., Alhmedi, A., […] Lemarquand, A., Cornille, A.* (2021). Experimental test for local adaptation of the rosy apple aphid (Dysaphis plantaginea) to its host (Malus domestica) and to its climate in Europe. PCI Ecology.
• Groppi, A.*, Liu, S.*, Cornille, A.*, […], Decroocq, V. (2021). Population genomics of apricots unravels domestication history and adaptive events. Nature Communications, 12(1), 1–16.
• Chalvin, C., Drevensek, S., Chollet, C., […], Cornille, A. (2021). Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant. PLOS ONE, e0248954.
• Koupilová, K., Koubek, T., Cornille, A., Janovský, Z. (2021). Local maladaptation of the anther-smut fungus parasitizing Dianthus carthusianorum. European Journal of Plant Pathology, 160(2), 365–374.
• İltaş, O., Koubek, T., Cornille, A., Schmickl, R., Lafon-Placette, C. (2021). Early evolution of reproductive isolation: A case of weak inbreeder/strong outbreeder leads to an intraspecific hybridization barrier in Arabidopsis lyrata. Evolution, 7, 1466–1476.
• Denoirjean, T., Doury, G., Cornille, A., Chen, X., Hance, T., Ameline, A. (2021). Genetic structure of Malus sylvestris and potential link with preference/performance by the rosy apple aphid pest Dysaphis plantaginea. Scientific Reports, 11, 5732.
• Hartmann, F. E., Snirc, A., Cornille, A., Godé, C., Touzet, P., Van Rossum, F., Fournier, E., Le Prieur, S., Shykoff, J., Giraud, T. (2020). Congruent population genetic structures and divergence histories in anther‐smut fungi and their host plants Silene italica and the Silene nutans species complex. Molecular Ecology, 29(6), 1154–1172.
• Liu, S.*, Cornille, A.*, Decroocq, S., Tricon, D., Chague, A., Eyquard, J.-P., Liu, W. S., Giraud, T., Decroocq, V. (2019). The complex evolutionary history of apricots: species divergence, gene flow and multiple domestication events. Molecular Ecology, 28, 5299–5314.
• Hartmann, F. E., Rodríguez de la Vega, R. C., Carpentier, F., Gladieux, P., Cornille, A., Hood, M. E., Giraud, T. (2019). Understanding adaptation, coevolution, host specialization and mating system by combining population and comparative genomics in castrating anther-smut fungi. Annual Review of Phytopathology, 57, 431–457.
• Cornille, A., Ferran, A., Garcia, E., Vernesi, C., Fietta, A., Brinkkemper, O., Kirleis, W., Schlumbaum, A., Roldán-Ruiz, I. (2019). A multifaceted overview of apple tree domestication. Trends in Plant Science, 24(8), 770–782.
• Peace, C. P., Troggio, M., van de Weg, E., Howard, N. P., Cornille, A., …, Vanderzande, S. (2019). Apple whole genome sequences: recent advances and new prospects. Horticulture Research, 6(1), 59.
• Ruhsam, M., Jessop, W., Cornille, A., Renny, J., Worrell, R. (2018). Crop-to-wild introgression in the European wild apple Malus sylvestris in Northern Britain. Forestry. cpy033.
• Lafon-Placette, C., Hatorangan, M. R., Steige, K. A., Cornille, A., Lascoux, M., Slotte, T., Köhler, C. (2018). Paternally expressed imprinted genes associate with hybridization barriers in Capsella. Nature Plants, 4, 352–357.
• Amirchakhmaghi, N., Yousefzadeh, H., Hosseinpour, B., Espahbodi, K., Aldaghi, M., Cornille, A. (2018). First insight into genetic diversity and population structure of the Caucasian wild apple in the Hyrcanian forest (Iran) and its resistance to apple scab and powdery mildew. Genetic Resources and Crop Evolution, 65(4), 1255–1268.
• Besnard, G., Terral, J. F., Cornille, A. (2018). On the origins and domestication of the olive: a review and perspectives. Annals of Botany, 121(3), 385–403.
• Petit, E., Silver, C., Cornille, A., […], Hood, M. (2017). Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts. Molecular Ecology, 26(7), 1877–1890.
• Feurtey, A., Cornille, A., Shykoff, J. A., Snirc, A., Giraud, T. (2017). Crop-to-wild gene flow and its fitness consequences on a wild fruit tree: towards a comprehensive conservation strategy of the wild apple in Europe. Evolutionary Applications, 10(2), 180–188.
• Decroocq, S., Cornille, A., Tricon, D., Babayeva, […], Decroocq, V. (2016). New insights into the history of domesticated and wild apricot and its contribution to Plum pox virus resistance. Molecular Ecology, 19, 4712–4729.
• Feurtey, A., Gladieux, P., Hood, M. E., Snirc, A., Cornille, A., Rosenthal, L., Giraud, T. (2016). Strong phylogeographic costructure between the anther-smut fungus and its white campion host. New Phytologist, 212(3), 668–679.
• Kryvokhyzha, D.*, Holm, K.*, Chen, J., Cornille, A., Glémin, S., Wright, S., Lagercrantz, U., Lascoux, M. (2016). The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). Molecular Ecology, 25, 106–1121.
• Cornille, A., Salcedo, A., Kryvokhyzha, D., Holm, K., Wright, S., Lascoux, M. (2016). Successful history of colonization of the worldwide tetraploid Capsella bursa-pastoris in Eurasia. Molecular Ecology, 5, 616–629.
• Yao, J.L., Xu, J., Cornille, A., […], Gleave, A. (2015). A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal, 84(2), 417–427.
• Leforestier D., Ravon E., Muranty H., Cornille A., Lemaire C., Giraud G., Durel C.E., Branca A. (2015). Genomic bases of the differences between cider and dessert apple varieties. Evolutionary Applications, 8(7):650–661.
• Cornille A.*, Feurtey A., Gélin U., Gladieux P., Giraud T. (2015). Gene flow in a temperate wild fruit tree: conservation and breeding implications. Evolutionary Applications, 8(4):373–384. *Corresponding author.*
• Cornille A., Gladieux P., Giraud T. (2014). Diversification in the genus Malus. Acta Botanica Gallica.
• Schnitzler A., Arnold C., Cornille A., Olivier X., Schnitzler C. (2014). Wild European apple population dynamics: insights from genetics and ecology in the Rhine Valley. PLoS ONE, 9(5):e96596.
• Cornille A.*, Giraud T., Smulders M.J.M., Roldán-Ruiz I., Gladieux P. (2014). The domestication and evolutionary ecology of apples. Trends in Genetics, 30(2):57–65. *Corresponding author.*
• Yuan J., Cornille A., Giraud T., Zhou S.L., Cheng F.Y. (2014). Independent domestications of cultivated tree peonies. Molecular Ecology, 23:82–95.
• Cornille A., Giraud T., Bellard C., Tellier A., Le Cam B., Smulders M.J.M., Kleinschmit J., Roldan-Ruiz I., Gladieux P. (2013). Post-glacial recolonization history of the European crabapple. Molecular Ecology, 22(8):2249–2263.
• Cornille A., Gladieux P., Giraud T. (2013). Crop-to-wild gene flow in the closest wild relatives of cultivated apple. Evolutionary Applications, 5:694–704.
• Cornille A.*, Gladieux P., Roldan-Ruiz I., Laurens F., Le Cam B., Smulders R., Nersesyan A., Clavel J., Olonova M., Feugey L., Gabrielian I., Xiu-Guo Z., Tenaillon M., Giraud T. (2012). New insights into the history of domesticated apples. PLoS Genetics, 8(5):e1002703. *Corresponding author.*
• Lê Van A., Gladieux P., Lemaire C., Cornille A., Giraud T., Durel C-E., Caffier V., Le Cam B. (2012). Evolution of pathogenicity traits in the apple scab fungal pathogen. Evolutionary Applications, 5:694–704.
• Cornille A.*, Underhill J.G., Cruaud A., Hossaert-McKey M., Johnson S.D., Tolley K.A., Kjellberg F., van Noort S., Proffit M. (2012). Floral volatiles, pollinator sharing and diversification in the fig-wasp mutualism. Proceedings of the Royal Society B, 279:1731–1739. *Corresponding author.*
• Peace C.P., Troggio M., van de Weg E., Howard N.P., Cornille A., Durel C.-E., Bianco L., Micheletti D., Pagliarani G., Velasco R., Tartarini S., Gardiner S.E., Laurens F., Costa F., & Vanderzande S. (2019). Apple whole genome sequences: recent advances and new prospects. Horticulture Research, 6(1):59.
• Ruhsam M., Jessop W., Cornille A., Renny J., Worrell R. (2018). Crop-to-wild introgression in the European wild apple Malus sylvestris in Northern Britain. Forestry, cpy033.
• Lafon-Placette C., Hatorangan M.R., Steige K.A., Cornille A., Lascoux M., Slotte T., Köhler C. (2018). Paternally expressed imprinted genes associate with hybridization barriers in Capsella. Nature Plants, 4:352–357.
• Amirchakhmaghi N, Yousefzadeh H., Hosseinpour B., Espahbodi K., Aldaghi M., Cornille A. (2018). First insight into genetic diversity and population structure of the Caucasian wild apple in the Hyrcanian forest (Iran)… Genetic Resources and Crop Evolution, 65(4):1255–1268.
• Besnard G., Terral J.F., Cornille A. (2018). On the origins and domestication of the olive: a review and perspectives. Annals of Botany, 121(3):385–403.
• Petit E., Silver C., Cornille A., Rodríguez de la Vega R.C., Hood M.E. (2017). Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts. Molecular Ecology, 26(7):1877–1890.
• Feurtey A., Cornille A., Shykoff J.A., Snirc A., Giraud T. (2017). Crop-to-wild gene flow and its fitness consequences on a wild fruit tree. Evolutionary Applications, 10(2):180–188.
• Decroocq S., Cornille A., Tricon D., Babayeva S., Chague A., Eyquard J.P., & Decroocq V. (2016). New insights into the history of domesticated and wild apricot. Molecular Ecology, 19:4712–4729.
• Feurtey A., Gladieux P., Hood M.E., Snirc A., Cornille A., Rosenthal L., Giraud T. (2016). Strong phylogeographic costructure between the anther-smut fungus and its white campion host. New Phytologist, 212(3):668–679.
• Kryvokhyzha D.*, Holm K.*, Chen J., Cornille A., Glémin S., Wright S., Lagercrantz U., Lascoux M. (2016). The influence of population structure on gene expression and flowering time variation… Molecular Ecology, 25:106–1121. *Contributed equally.*
• Cornille A.*, Salcedo A., Kryvokhyzha D., Holm K., Wright S., Lascoux M. (2016). Successful history of colonization of the worldwide tetraploid Capsella bursa-pastoris in Eurasia. Molecular Ecology, 5:616–629. *Corresponding author.*
• Yao J.L., Xu J., Cornille A., Tomes S., McGhie T.K., Weskett R., Allan A.C., Gleave A. (2015). A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal, 84(2):417–427.
• Leforestier D., Ravon E., Muranty H., Cornille A., Lemoine M., Giraud T., Branca A. (2015). Genomic bases of the differences between cider and dessert apple varieties. Evolutionary Applications, 8(7):650–661.
• Cornille A.*, Feurtey A., Gélin U., Gladieux P., Giraud T. (2015). Gene flow in a temperate wild fruit tree: conservation and breeding implications. Evolutionary Applications, 8(4):373–384. *Corresponding author.*
• Cornille A., Gladieux P., Giraud T. (2014). Diversification in the genus Malus. Acta Botanica Gallica.
• Schnitzler A., Arnold C., Cornille A., Olivier X., Schnitzler C. (2014). Wild European apple population dynamics: insights from genetics and ecology in the Rhine Valley. PLoS ONE, 9(5):e96596.
• Cornille A.*, Giraud T., Smulders M.J.M., Roldán-Ruiz I., Gladieux P. (2014). The domestication and evolutionary ecology of apples. Trends in Genetics, 30(2):57–65. *Corresponding author.*
• Yuan J., Cornille A., Giraud T., Zhou S.L., Cheng F.Y. (2014). Independent domestications of cultivated tree peonies. Molecular Ecology, 23:82–95.
• Cornille A., Giraud T., Bellard C., Tellier A., Le Cam B., Smulders M.J.M., Kleinschmit J., Roldan-Ruiz I., Gladieux P. (2013). Post-glacial recolonization history of the European crabapple. Molecular Ecology, 22(8):2249–263.
• Cornille A., Gladieux P., Giraud T. (2013). Crop-to-wild gene flow in the closest wild relatives of cultivated apple. Evolutionary Applications, 5:694–704.
• Cornille A.*, Gladieux P., Roldan-Ruiz I., Laurens F., Le Cam B., Smulders M.J.M., Durel C.E., Giraud T. (2012). New insights into the history of domesticated apples. PLoS Genetics, 8(5):e1002703. *Corresponding author.*
• Lê Van A., Gladieux P., Lemaire C., Cornille A., Giraud T., Le Cam B. (2012). Evolution of pathogenicity traits in the apple scab fungal pathogen. Evolutionary Applications, 5:694–704.
• Cornille A.*, Underhill J.G., Cruaud A., Hossaert-McKey M., Johnson S.D., Tolley K.A., Kjellberg F., van Noort S., Proffit M. (2012). Floral volatiles, pollinator sharing and diversification in the fig-wasp mutualism. Proceedings of the Royal Society B, 279:1731–1739. *Corresponding author.*

📘 Book Chapters

• Gayle V., Cornille A. (2018). Genetic Diversity and Domestication History in Pyrus. In: The Pear Genome. Compendium of Plant Genome. Springer. Springer Link
• Volk G., Cornille A., Durel C.E., Gutierrez B. (2021). Botany, Taxonomy, and Origins of the Apple. In: The Apple Genome, pp. 19–32. Springer. Springer Link

🧪 Protocols

• Maret T., Venon A., Cornille A. Apple Leaf Field Collection Protocol for Enzymatic Methyl-seq. View Protocol (2026)
• Cornille A., Dadole R., Venon A. DNA extraction from apple leaves or apple buds. View Protocol (2025)
• Venon A., Dadole R., Cornille A. High Molecular Weight (HMW) DNA extraction from apple leaves for nanopore long-read sequencing. View Protocol (2024)
• Brisson M., Cornille A. FruitRescue! – Prunus phenotyping. View Protocol (2021)
• Brisson M., Cornille A. FruitRescue! – Apple phenotyping. View Protocol (2021)